Abstract

Next-generation sequencing (NGS) efforts have established catalogs of mutations relevant to cancer development. However, the clinical utility of this information remains largely unexplored. Here, we present the results of the first eight patients recruited into a clinical whole-genome sequencing (WGS) program in the United Kingdom. We performed PCR-free WGS of fresh frozen tumors and germline DNA at 75× and 30×, respectively, using the HiSeq2500 HTv4. Subtracted tumor VCFs and paired germlines were subjected to comprehensive analysis of coding and noncoding regions, integration of germline with somatically acquired variants, and global mutation signatures and pathway analyses. Results were classified into tiers and presented to a multidisciplinary tumor board. WGS results helped to clarify an uncertain histopathological diagnosis in one case, led to informed or supported prognosis in two cases, leading to de-escalation of therapy in one, and indicated potential treatments in all eight. Overall 26 different tier 1 potentially clinically actionable findings were identified using WGS compared with six SNVs/indels using routine targeted NGS. These initial results demonstrate the potential of WGS to inform future diagnosis, prognosis, and treatment choice in cancer and justify the systematic evaluation of the clinical utility of WGS in larger cohorts of patients with cancer.

Identification of somatic and germline variants in genes from the DNA damage response (DDR) pathway from Cases 1–8. Graphical representation of the variants identified by WGS in 22 DDR pathway genes in cancer Cases 1–8. A and B show somatic and germline variants, respectively, for each cancer case. Each bar or track on the horizontal axis represents a different cancer case and the 22 individual DDR genes are represented on the vertical axis. CNAs, indels, and SNVs are represented by circles, squares, and diamonds, respectively. The color key indicates more detail about the type of variant (e.g., a red circle represents a homozygous copy-number loss). Only disruptive somatic or germline SNVs and indels are included, whereas for germline variants (B) only SNVs with minor allele frequency of <6% are included. Case 1 includes a somatic missense SNV and a cnLOH region involving TP53, as well as copy-number loss of PTEN and allelic imbalance of BRCA2. Case 2 presents copy-number aberrations overlapping various DDR genes, but no SNVs, indels, or copy-number events involving TP53. Case 3 includes TP53 mutations, an allelic imbalance involving TP53, BRCA1, BRIP1, RAD51C, and RAD51D, and a single loss involving FANCA. In Case 4, WGS detected a germline deleterious SNV in RAD51B, together with a somatic CN loss in the same locus. Case 5 includes somatic mutations in various DDR genes but no copy-number aberrations, whereas RAD54L and ATM in the germline are affected by a region of homozygosity and a missense mutation, respectively. Case 6 has a frameshift mutation and a CN loss involving TP53 and, importantly, a somatic homozygous CN loss encompassing BRCA2. In Case 7, most DDR genes are affected by a somatic CN loss or gain, whereas the germline includes missense mutations in FANCI, RAD54L, RAD51B, and PARP1. Finally, in Case 8, PTEN and BRCA2 are affected by somatic CN losses, and ATM includes a splice site mutation in the germline. See the main text for more details.